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In my build i have a graphics card which has pcie express 3.0 x16 (gtx 960). I have just noticed the motherboard i use only supports pcie express 2.0 in the x16 slot. Will this make a big performance difference? If so can you suggest a micro ATX board i could use. Will need AM3+ chipset.

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It should be fine.

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It is entirely OK and will (probably) be for the foreseeable future.

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In my build i have a graphics card which has pcie express 3.0 x16 (gtx 960). I have just noticed the motherboard i use only supports pcie express 2.0 in the x16 slot. Will this make a big performance difference? If so can you suggest a micro ATX board i could use. Will need AM3+ chipset.

At X16 it wont make any difference for your card, PCI-e 3.0 doesn't really benefit graphics cards(unless low link speeds like X4, or SLI/CFX). You will be fine with PCI-e 2.0/2.1

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